Salmonid_MHC_classifier

IPD-MHC classifier for Salmonids

Dependencies

Muscle, emboss (transep and water tools) which can installed with Conda as below

$ conda install muscle emboss

Uses os, sys, subprocess, Bio and ete3 packages in python. First three packages are available within python while the last two can be installed with Conda as below

$ conda install -c conda-forge biopython ete3 

Initiation

$ python mhc_fetch.py

This downloads the up-to-date sequences from the IPD-MHC fish database and creates three files in a new folder called "data" This need not be executed everytime but it is good to use this to update the sequences periodically. If so, delete the folder "data" and re-run the above command.

$ python salmonid_mhc_classifier.py [input.fa] [output_folder] [report.txt] [Db_name]

input.fa: Sequences in fasta format
output_folder: Folder for output data report.txt: Name for the output report file
Db_name: Sasa-DAA, Sasa-DAB, Sasa-UAB, Onmy-DAA, Onmy-DAB, Onmy-UAB

Execution

Output files are saved to the [output_folder] as specified in the Each fasta record in the [input.fa] will be processed one at a time
Output: NAME.fa

Nucleotide record is translated into peptide
Output: NAME.aa

Nucleotide record is aligned with the relevant [Db_name] using muscle
Output: NAME_muscle_output.tree.txt and NAME_muscle_output.aln.txt

Muscle tree is converted to png using ete3
Output: NAME_muscle_output.tree.png

Sibligns in two neighbouring clades are extracted using ete3 Output: Detail in [report.txt]

Local alignment in performed between the query and each of the siblings at nucleotide and peptide level using Water
Output NAME_SIBLINGS_water_nt.txt and aa_txt

Sequence similarity and identity information from Water are included in the report
Output: Detail in [report.txt]

Output

The script replaces '-' with '_' for all the identifiers since it interferes with the tree analysis part of the script. The output will reflect this. For example, Sasa-DAA*0601 will become Sasa_DAA*0601.

Example output is provide in the folder output_example

Tool versions

The pipeline has been tested with the following versions:
Muscle v3.8.1551
transeq, water: EMBOSS v6.6.0.0
ete3 v3.1.1